Search Results (9,193)

Soybean (Glycine max) is relatively recalcitrant to genetic manipulations; hence, it is often interrogated with transient means such as virus-induced gene silencing (VIGS). We earlier modified cowpea severe mosaic virus (CPSMV) to develop a soybean-friendly VIGS system referred to as QUIN-FZ. Here we report additional calibrations of this system. We enhanced the intra-bacterial stability of plasmid QUIN, which contained a CPSMV RNA1 cDNA embedded with four introns, by adding a fifth intron, resulting in PENTIN. We separately upgraded the plasmid FZ, which contained a modified CPSMV RNA2 cDNA with a cloning site in the middle of the viral polyprotein, by creating another cloning site within the 3′ untranslated region, leading to ZY. We next used the new PENTIN-ZY system to investigate a putative soybean protein kinase designated QL18. Virus-mediated overexpression of two allelic, 147-amino-acid (aa) protein fragments, derived from two different QL18 orthologs, elicited drastically different responses in soybeans. While the fragment derived from soybean accession OX20-8 prevented the cognate virus from infecting top young leaves in at least 50% of inoculated seedlings, its allelic counterpart derived from soybean accession PI427105B elicited apical necrosis in 100% of soybean seedlings. By examining progeny viruses as well as viruses encoding chimeras of the two fragments, we identified more than a dozen mutations that abrogated these unique phenotypes. Our findings establish the PENTIN-ZY system as a versatile tool for overexpressing small proteins and protein fragments, accelerating their functional characterization. Full article

Soil salinity remains a major constraint to rice productivity, particularly during early developmental stages when plants are highly sensitive to osmotic and ionic stress. In this study, we evaluated 201 genetically diverse rice genotypes from the 3K Rice Diversity Panel to investigate stage-specific mechanisms of salinity tolerance and develop machine learning-based predictive models for rapid phenotypic screening. Morphological and physiological traits were measured under control and saline conditions at germination and early seedling stages to derive Stress Tolerance Indices (STIs). The average membership function value (AMFV), calculated from multi-trait STI profiles, effectively captured variation in salinity responses and enabled classification of genotypes into five tolerance categories. Genome-wide association analysis using high-density SNP markers identified 36 significant marker–trait associations, including potentially novel SNPs on chromosomes 1 and 12. Several loci co-localized with candidate genes (LTR1, LGF1, OsCPS4, OsNCX7, and OsNHX4), while functional SNPs within genes (OsDRP2C, RLCK168, and OsMed37_2) and non-synonymous variants (qSVII11.1 and qSNaK3.1) further supported their candidacy in salinity tolerance. Mining favourable SNPs of causal genes identified superior multilocus combinations consistent with STI-based phenotypic patterns, with genotype 91-382 emerging as the strongest performer, exhibiting enhanced Na⁺ exclusion, K⁺ retention, and biomass resilience across developmental stages. To address multicollinearity among STI traits, we applied cross-validated LASSO (germination) and Elastic Net (early seedling) models, achieving high predictive accuracy and revealing a developmental shift from biomass-driven tolerance at germination to ion-regulatory processes at the seedling stage. Independent validation showed strong agreement between predicted and observed AMFVs. By integrating physiological indices, GWAS-derived SNP signals, and regularized machine learning approaches, this study provides a robust framework for identifying elite donors and accelerating breeding for salt-tolerant rice. Full article

The collection of high-quality seeds to produce forest seedlings is closely linked with the time of harvesting. Climate warming is already having visible effects in all life stages of forest tree species, including the timing of seed maturation. The purpose of this study was to update the knowledge on seed collection timing and to identify the indicators of physiological maturity for three key Eastern European tree species—silver fir (Abies alba), European larch (Larix decidua), and small-leaved lime (Tilia cordata). Seeds and cones were collected from Romanian clonal seed orchards and evaluated at several stages of seed maturation using germination tests for European larch and tetrazolium viability tests for silver fir and small-leaved lime. The results revealed species-specific differences in seed maturation timing: in silver fir seed viability increased slightly from late August to early September, in European larch germination remained low (≈20%) regardless of harvest time, while small-leaved lime viability declined significantly after late August. These findings suggest that the harvest period observed during the study years occurred earlier than the traditionally recommended intervals and could be linked to recent warming trends. This study highlights the relevance of re-evaluating seed collection schedules under changing climatic conditions, while further multi-year studies are required to confirm these patterns and refine practical recommendations. Full article

Avocado (Persea americana Mill.) is one of the most widely consumed fruit tree crops worldwide, with cultivation expanding rapidly beyond its Mesoamerican and northwest South America center of origin. In emerging secondary diversity centers such as East Africa, farmers have long propagated seedling naturalized populations that may hold valuable reservoirs of genetic diversity, yet these resources remain underexplored. To help fill this gap, this study developed the first genomic resources for avocados in Tanzania, where avocado has a long history of introduction and diversification dating to the first Arab incursions and Catholic missionary missions. Low-coverage whole-genome resequencing (lcWGS) data were obtained from 95 trees sampled in Tanzania across the low- to mid-altitude Morogoro region (n = 25) and the Southern Highlands—i.e., the Iringa (n = 20), Mbeya (n = 30) and Ruvuma (n = 20) regions. In order to guide racial assignation, sequences were merged with NCBI-available lcWGS data from 205 avocado trees, including 42 commercial varieties, with reported ancestry. Population stratification as inferred via maximum likelihood phylogenetic inference, genetic principal component analysis, and ADMIXTURE unsupervised clustering suggested that the sampled Tanzanian avocado trees were genetically closer to the West Indian race and more distant from the northwest South American Caribbean and Andean groups. Additionally, while the trees from the low- to mid-altitude region of Morogoro were almost exclusively West Indian type, some trees from the Southern Highlands aligned more closely with West Indian × Guatemalan and West Indian × Mexican hybrids. These trends were equally supported by a subset of 10,460 high-coverage (10×) SNP markers. Together these findings clarify the dynamics of avocado diversification in a secondary center in East Africa, spanning recent introductions from a single Mesoamerican race, adaptation to a wide range of locally geographic conditions, and farmer-driven selection matching local tribal preferences. Characterizing these locally adapted resources is key for identifying underrepresented yet promising provenances, developing resilient and sustainable horticultural production systems, and safeguarding the species’ global genetic heritage. Full article

Apple pomace represents an important agro-industrial residue with high moisture content and significant environmental burden if improperly managed. This study investigated its thermochemical valorisation into biochar via two processes, followed by comprehensive physicochemical characterization and agronomic evaluation. Elemental analysis revealed carbon enrichment from 47.89% in raw material to 77–78% after the thermal process, evidencing a progressive aromatization. Scanning electron microscopy, Fourier transform infrared spectroscopy, and Raman analysis confirmed a temperature-dependent transition from partially amorphous carbon (400 °C) to more ordered aromatic structures (450 °C), while excessive thermal treatment (550 °C) increased structural defects. ICP-OES revealed an enrichment in thermally stable metals (Fe, Al, Mn) and limited Cd accumulation. Germination assays using Triticum aestivum L. demonstrated that biochar produced at 400 °C significantly improved the germination uniformity and seedling height (14.1 mm), as well as biomass accumulation compared to the control soil sample. The fertilizer addition increased the soluble Na and electrical conductivity (up to 643 µS/cm), potentially inducing transient salinity stress. Soil chemical analysis indicated increased K availability in soils amended with biochar produced at 400 °C, whereas the combination of biochar obtained at 450 °C with fertilizer conducted to elevated concentrations of certain trace metals, mainly Ni and Cr, highlighting the demand for careful monitoring. Overall, the biochar produced at 400 °C yielded to an optimal balance between structural stability, nutrient enrichment, and agronomic performance, evidencing that apple pomace may be a viable feedstock for sustainable biochar production within circular bioeconomy frameworks. Full article

Background/Objectives: Having longer mesocotyls is beneficial for the deep-sowing tolerance of rice, which is important for seedling establishment. Methods: Here, we performed transcriptome analysis of the elongating mesocotyl of Zhengdao 209 in response to three different sowing depths to identify the pivotal genes regulating rice mesocotyl elongation. Results: Three groups with different mesocotyl lengths were compared using transcriptome analysis, and 60 common differentially expressed genes were detected. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses revealed that these genes are primarily involved in phenylpropanoid biosynthesis, cutin suberine and wax biosynthesis, the plant mitogen-activated protein kinase signaling pathway, diterpenoid biosynthesis, cyanoamino acid metabolism, carbon fixation in photosynthetic organisms, flavonoid biosynthesis, and glutathione metabolism. Furthermore, weighted gene co-expression network and hierarchical clustering analyses showed that most of the differentially expressed genes are implicated in phenylpropanoid biosynthesis, carbon metabolism, photosynthesis antenna proteins, and plant–pathogen interactions. Among the genes involved in phenylpropanoid biosynthesis processes, the expression levels of OsPHT3 and LOC_Os04g59260 increased, while OsCCR1, OsPGIP4, and LOC_Os01g45110 expression decreased with increasing sowing depth. Among the genes involved in the mitogen-activated protein kinase signaling pathway, the expression levels of LOC_Os07g03319 and LOC_Os07g03580 increased, while LOC_Os07g03409 decreased with increasing sowing depth. Among the genes involved in diterpenoid biosynthesis processes, the expression levels of OsCYP76M5 and OsCYP71Z2 decreased, while OsCYP71Z21 increased with increasing sowing depth. Furthermore, the expression levels of these genes were analyzed using quantitative real-time polymerase chain reaction, which confirmed the transcriptome analysis results. Conclusions: This study identified candidate genes governing rice mesocotyl length and provides novel insights into the molecular regulatory mechanisms underlying mesocotyl elongation in rice. Full article

For the western Patagonia region (Argentina), climate change models predict a 1–3 °C increase in temperature and a 10%–30% reduction in precipitation. Patagonia native forests are home to a variety of soil fungi, including ectomycorrhizal fungi (EcM), which play a crucial role in drought-tolerant trees. However, the responses of soil fungi to changes in rainfall remain poorly understood. To evaluate shifts in soil fungal communities’ response under reduced precipitation scenarios and identify potentially drought-tolerant EcM species, we took 144 composite soil samples associated with Nothofagus forests along an east–west rainfall gradient. We used environmental DNA to estimate alpha and beta diversity of soil fungi and EcM. Soil fungal richness did not differ across precipitation treatments, whereas EcM richness declined with decreasing precipitation. Shannon and inverse Simpson indices of EcM decreased under reduced precipitation, whereas no significant effects were observed on soil fungi, highlighting the EcM vulnerability to water limitation. Soil fungi community composition changes along the rainfall gradient due to species replacement. Tarzetta sp., Cortinarius sp., and Russula sp. were found in drier plots, indicating a potential association with drought tolerance. Selecting native drought-tolerant EcM for forest management and restoration can improve seedling establishment and ecosystem resilience under climate change. Full article

Soil salinization poses a severe threat to global wheat production, yet the physiological mechanisms underlying photosynthetic responses to neutral, alkaline, and combined salt stress remain poorly understood. This study systematically evaluated the photosynthetic physiology and salt tolerance of six spring wheat genotypes under three types of salt stress at varying concentrations. By integrating phenotypic data, gas exchange parameters, chlorophyll fluorescence indices, and biomass measurements, and applying structural equation modeling and multivariate analysis, key traits regulating biomass were identified. The results revealed significant interactions among salt stress type, genotype, and concentration on photosynthetic parameters. Structural equation modeling analysis revealed that under neutral salt stress, both gas exchange parameters and chlorophyll content had significant direct effects on seedling biomass, with standardized path coefficients of 0.421 and 0.400, respectively. Under alkaline and combined salt stresses, only chlorophyll content showed a significant direct effect on biomass, with standardized path coefficients of 0.873 and 0.790, respectively. Multiple regression analysis further identified key photosynthetic factors influencing growth under different stress types. Under neutral salt stress, phi (Ro) and E significantly affected biomass, whereas under alkaline and combined salt stresses, biomass was primarily co-regulated by phi (Ro) and phi (Eo). Based on a comprehensive evaluation of salt tolerance index, damage index, and biomass response, genotypes W06 and W02 exhibited the strongest overall salt tolerance. This study systematically elucidates the differential response mechanisms of photosynthesis in spring wheat under distinct salt stress types, providing an important theoretical basis and elite germplasm resources for breeding salt-tolerant wheat varieties. Full article

Cymbidium goeringii, an important orchid species, holds significant aesthetic and commercial potential in horticulture. However, stem rot caused by Fusarium oxysporum has emerged as a major biological constraint hindering industry development. In this study, we isolated five endophytic fungal strains from C. goeringii roots—namely, DG3 (Bjerkandera), DG4 (Cylindrocarpon), CLG3 (Talaromyces), CLG6 (Clonostachys), and Z3 (Trichoderma)—and assessed their inhibitory efficacy against stem rot and their potential to promote growth in C. goeringii. In vitro assays indicated that all five fungal strains had the ability to fix nitrogen and produce indole-3-acetic acid, as well as the capability to produce protease and exert broad-spectrum antimicrobial effects. The five endophytic fungal strains exhibited stem rot-resistant effects, among which strain Z3 showed the best inhibitory effect against stem rot, with a control efficacy reaching 68.89%. Treatment of C. goeringii seedlings with these endophytic fungal fermentation broths for 100 d significantly promoted growth compared to the control. The fresh weight increased by 10.53% to 88.16%, and root activity was enhanced by 50% to 162.5%. Additionally, the plant height and the longest leaf length increased by up to 23.68% and 47.50%, respectively, compared to the control. Additionally, the total chlorophyll content was up to 25.34% higher than that of the control group, and the soluble protein content was up to 39.54% higher. The MDA content was reduced by up to 40.23% compared to the control group. These endophytes also regulated the activity of defense-related enzymes in C. goeringii, including delaying the decline in the activities of antioxidant enzymes such as superoxide dismutase, peroxidase, and catalase. These results highlight the potential of these five endophytic fungi as effective agents for managing stem rot in C. goeringii. Full article

Forest plantations, including those of Norway spruce, are increasingly threatened by drought in Central Europe. One of the measures understating this threat might be the use of drought-mitigative additives at planting. The effects of induced water limitation and the application of hydrogel Agrisorb and commercial ectomycorrhizal fungi (EMF) inoculum Ectovit on the development of 2 + 1 spruce seedlings were estimated in this study. The root systems of 2 + 0 seedlings were treated with the additives, along with their spring transplantation into peat-filled pots. The seedlings were then exposed throughout the entire growing season either to full watering (FW)—volumetric soil water content 70%, reduced watering (RW)—water content 40%, periodic watering (PW)—substrate rehydrated to 70% after drying to the wilting point (21%), or remained non-watered (NW). Survival, growth and chlorophyll fluorescence of the seedlings decreased proportionally to the increased drought intensity, while the highest root-to-shoot ratio and EMF colonization of roots occurred under PW and RW, respectively. NW seedlings died after 9 weeks of desiccation, whereas the EMF inoculum prolonged the survival time by one week. Ectomycorrhizas were formed predominantly with native EMF in all the treatments; nevertheless, compared with the uninoculated control, the formation of a treatment-specific EMF root morphotype and increased EMF colonization under PW and RW were observed on the inoculated seedlings. Both the EMF inoculum and the hydrogel increased survival under PW by approximately 15% but did not significantly affect growth, regardless of the watering regime. These results are limited to the experimental conditions and suggest a more dominant effects of the watering regimes compared with the additives tested. Full article

Poultry manure is a valuable nutrient source, but insufficient stabilisation may cause phytotoxic effects during early plant development. This study evaluated the phytotoxicity of fresh and composted poultry manure using seed germination and root elongation bioassays. Elutriates of aerated and static compost mixtures, poultry manure composts, and fresh manure were tested on sunflower (Helianthus annuus L.), mungbean (Vigna radiata L.), and white mustard (Sinapis alba L.). Germination and relative root growth indices were calculated. Aerated compost mixtures showed minimal phytotoxicity, whereas fresh and partially composted manure strongly inhibited seedling development. Mungbean was the most sensitive species. Root elongation was more sensitive than germination, confirming bioassays as reliable tools for assessing compost maturity and fertiliser safety. Full article

Microalgal and cyanobacterial biostimulants are increasingly recognized as sustainable tools for enhancing crop establishment and reducing dependence on synthetic agrochemicals. However, the strain-specific effects of many taxa on seed germination and early seedling development remain insufficiently characterized. This study evaluated the effects of seven microalgal and cyanobacterial suspensions on the germination kinetics and early seedling vigor of cucumber (Cucumis sativus L.). Several strains significantly accelerated germination and enhanced seedling performance relative to the control. Treatment with Coelastrella rubescens BCAC 301 S39, Scotinosphaera lemnae BCAC 113, Vischeria magna UTEX 2351, and Anabaena sp. IT4 significantly reduced mean germination time from 4.50 d to 2.23–2.29 d and advanced the time to 50% germination (T₅₀) from 4.0 to 2.0–2.1 d. These treatments also increased the germination index from 48.32 to 78.17–100.67 and enhanced seedling traits, including root length (32–53%), shoot length (≈29%), leaf length (17–21%), and fresh (30–43%) and dry biomasses (12–22%). Correlation analysis revealed strong positive associations between germination indices and seedling vigor parameters, indicating the faster germination promotes early growth. In conclusion, the results demonstrate that specific microalgal strains can function as effective seed-phase biostimulants, offering a sustainable strategy to enhance germination uniformity, early seedling establishment, and crop productivity. Full article

Salinity stress impairs maize growth by inducing osmotic stress, pigment degradation, and ionic imbalance, particularly during early seedling development. This study investigated the morpho-physiological and ionic responses of different maize genotypes exposed to increasing salinity levels (control, 3, 6, and 9 dS/m) at the seedling stage. Salinity caused a reduction in biomass accumulation (shoot fresh weight and shoot dry weight), plant height, and K⁺/Na⁺ ratio, with pronounced effects under severe stress. Significant genotypic variability was detected for photosynthetic pigments (chlorophyll a, chlorophyll b, total chlorophyll and carotenoids) growth traits, and ionic regulation, indicating diverse physiological adaptation strategies. Stress tolerance indices and multivariate analysis revealed that chlorophyll stability, carotenoid accumulation, and maintenance of ionic homeostasis (K⁺/Na⁺ ratio) were the dominant physiological determinants of salinity tolerance. Additionally, principal component analysis showed a shift from biomass-driven variation under non-stress conditions to pigment- and ion-driven variation under higher salinity. Based on the results, genotypes BML 6 and HKI 163 maintained higher pigment content and improved K⁺/Na⁺ balance, enabling better growth under saline conditions. These findings highlight key physiological traits underlying salinity tolerance and provide insight into early-stage adaptive mechanisms in maize. Full article

Drought is a major constraint on crop productivity, and microbial inoculants are increasingly explored to mitigate plant water stress. However, most inoculant discovery pipelines rely on trait-based screening performed outside the ecological context in which beneficial plant-microbe interactions naturally arise. In natural soils, drought-exposed plants can reshape the rhizosphere environment by altering carbon allocation and root exudation, thereby selectively recruiting microorganisms compatible with water-limited conditions and effectively performing an ecological pre-selection. Here, we captured this process during early seedling establishment and leveraged drought-driven rhizosphere recruitment as a nature-guided strategy to nominate bacterial inoculant candidates. Tomato seedlings were grown in natural agricultural soil microcosms under well-watered and drought-stressed regimes, and cultivable bacteria were comparatively isolated from rhizosphere and bulk soil fractions. Recruitment-prioritized isolates were subsequently characterized through biochemical assays and genome-informed analyses to provide functional and taxonomic context and were evaluated in early inoculation assays under water stress. Drought-recruited isolates displayed distinct plant-associated responses, and genome-scale taxonomy indicated that one drought-associated isolate represents a genomically distinct lineage within the genus Paracoccus. Together, these findings highlight drought-driven rhizosphere recruitment as an ecologically grounded framework for identifying stress-compatible bacterial candidates and uncovering previously undescribed rhizosphere diversity. Full article